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Independent Section

Contains tests that are independent of the class of modeled organism, a model's complexity or types of identifiers that are used to describe its components. Parameterization or initialization of the network is not required. See readme for more details.

Consistency

Stoichiometric Consistency

100.0%

Mass Balance

98.1%

Charge Balance

100.0%

Metabolite Connectivity

100.0%

Unbounded Flux In Default Medium

97.0%

Sub Total

99%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{98.15 + 96.97 + (3 \cdot 100) +}{(5 \cdot 100)} = 99.30$ $(98.15 + 96.97 + (3 * 100) + )/((5 * 100)) = 99.30$

Annotation - Metabolites

Presence of Metabolite Annotation

4.1%

This test checks if any annotations at all are present in the SBML annotations field for each metabolite, irrespective of the type of annotation i.e. specific database cross-references, ontology terms, additional information. For this test to pass the model is expected to have metabolites and each of them should have some form of annotation. Implementation: Check if the annotation attribute of each cobra.Metabolite object of the model is unset or empty.

A total of 539 metabolites (95.91%) lack any form of annotation: o2_e, pydx_e, pro__L_e, hco3_e, lac__D_e, ...

Metabolite Annotations Per Database

pubchem.compound

0.0%

kegg.compound

4.1%

seed.compound

0.0%

inchikey

0.0%

inchi

0.0%

chebi

0.0%

hmdb

0.0%

reactome

0.0%

metanetx.chemical

0.0%

bigg.metabolite

0.0%

biocyc

0.0%

Metabolite Annotation Conformity Per Database

pubchem.compound

0.0%

kegg.compound

100.0%

seed.compound

0.0%

inchikey

0.0%

inchi

0.0%

chebi

0.0%

hmdb

0.0%

reactome

0.0%

metanetx.chemical

0.0%

bigg.metabolite

0.0%

biocyc

0.0%

Uniform Metabolite Identifier Namespace

100.0%

Sub Total

28%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{4.09 + 4.09 + (2 \cdot 100) + (20 \cdot 0)}{(24 \cdot 100)} = 28.39$ $(4.09 + 4.09 + (2 * 100) + (20 * 0))/((24 * 100)) = 28.39$

Annotation - Reactions

Presence of Reaction Annotation

5.7%

Reaction Annotations Per Database

rhea

0.0%

kegg.reaction

5.7%

seed.reaction

0.0%

metanetx.reaction

0.0%

bigg.reaction

0.0%

reactome

0.0%

ec-code

0.0%

brenda

0.0%

biocyc

0.0%

Reaction Annotation Conformity Per Database

rhea

0.0%

kegg.reaction

100.0%

seed.reaction

0.0%

metanetx.reaction

0.0%

bigg.reaction

0.0%

reactome

0.0%

ec-code

0.0%

brenda

0.0%

biocyc

0.0%

Uniform Reaction Identifier Namespace

100.0%

Sub Total

29%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{5.66 + 5.66 + (2 \cdot 100) + (16 \cdot 0)}{(20 \cdot 100)} = 29.35$ $(5.66 + 5.66 + (2 * 100) + (16 * 0))/((20 * 100)) = 29.35$

Annotation - Genes

Presence of Gene Annotation

100.0%

Gene Annotations Per Database

refseq

0.0%

uniprot

0.0%

ecogene

0.0%

kegg.genes

0.0%

ncbigi

0.0%

ncbigene

0.0%

ncbiprotein

100.0%

ccds

0.0%

hprd

0.0%

asap

0.0%

Gene Annotation Conformity Per Database

refseq

0.0%

uniprot

0.0%

ecogene

0.0%

kegg.genes

0.0%

ncbigi

0.0%

ncbigene

0.0%

ncbiprotein

100.0%

ccds

0.0%

hprd

0.0%

asap

0.0%

Sub Total

40%

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{(3 \cdot 100) + (18 \cdot 0)}{(21 \cdot 100)} = 40.00$ $((3 * 100) + (18 * 0))/((21 * 100)) = 40.00$

Annotation - SBO Terms

Metabolite General SBO Presence

0.0%

Metabolite SBO:0000247 Presence

0.0%

Reaction General SBO Presence

0.0%

Metabolic Reaction SBO:0000176 Presence

0.0%

Transport Reaction SBO:0000185 Presence

0.0%

Exchange Reaction SBO:0000627 Presence

0.0%

Demand Reaction SBO:0000628 Presence

Skipped

Sink Reactions SBO:0000632 Presence

Skipped

Gene General SBO Presence

0.0%

Gene SBO:0000243 Presence

0.0%

Biomass Reactions SBO:0000629 Presence

0.0%

Sub Total

The Sub Total is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{(11 \cdot 0)}{(11 \cdot 100)} = 0.00$ $((11 * 0))/((11 * 100)) = 0.00$

Total Score

45%

The Total Score is the result of the following calculation. For more information please click on "Readme" in the top left of the report.

$\frac{(3 \cdot 99.30) + (1 \cdot 28.39) + (1 \cdot 29.35) + (1 \cdot 40.00) + (2 \cdot 0.00)}{(3 \cdot 100) + (1 \cdot 100) + (1 \cdot 100) + (1 \cdot 100) + (2 \cdot 100)} = 45.12$ $((3 * 99.30) + (1 * 28.39) + (1 * 29.35) + (1 * 40.00) + (2 * 0.00))/((3 * 100) + (1 * 100) + (1 * 100) + (1 * 100) + (2 * 100)) = 45.12$

Total Score

45%

Score per Category

Specific Section

Covers general statistics and specific aspects of a metabolic network that are not universally applicable. See readme for more details.

SBML

SBML Level and Version

Errored

This test reports if the model file is represented in the latest edition (level) of the Systems Biology Markup Language (SBML) which is Level 3, and at least version 1. Implementation: The level and version are parsed directly from the SBML document.

FBC enabled

Errored

The Flux Balance Constraints (FBC) Package extends SBML with structured and semantic descriptions for domain-specific model components such as flux bounds, multiple linear objective functions, gene-protein-reaction associations, metabolite chemical formulas, charge and related annotations which are relevant for parameterized GEMs and FBA models. The SBML and constraint-based modeling communities collaboratively develop this package and update it based on user input. Implementation: Parse the state of the FBC plugin from the SBML document.

Basic Information

Model Identifier

iCC390

Total Metabolites

562

Total Reactions

618

Total Genes

389

Total Compartments

Metabolic Coverage

1.59

Metabolite Information

Unique Metabolites

490

Duplicate Metabolites in Identical Compartments

Metabolites without Charge

Metabolites without Formula

Medium Components

Reaction Information

Purely Metabolic Reactions

454

Purely Metabolic Reactions with Constraints

Transport Reactions

Transport Reactions with Constraints

Thermodynamic Reversibility of Purely Metabolic Reactions

1.00

Reactions With Partially Identical Annotations

0.00

Duplicate Reactions

0.00

Reactions With Identical Genes

0.48

Gene-Protein-Reaction (GPR) Associations

Reactions without GPR

Fraction of Transport Reactions without GPR

0.30

Enzyme Complexes

Biomass

Biomass Reactions Identified

Biomass Consistency

0.00

Biomass Production In Default Medium

0.15

Unrealistic Growth Rate In Default Medium

false

Biomass Production In Complete Medium

45.69

Blocked Biomass Precursors In Default Medium

Blocked Biomass Precursors In Complete Medium

Ratio of Direct Metabolites in Biomass Reaction

0.00

Number of Missing Essential Biomass Precursors

Energy Metabolism

Non-Growth Associated Maintenance Reaction

Growth-associated Maintenance in Biomass Reaction

true

Number of Reversible Oxygen-Containing Reactions

Erroneous Energy-generating Cycles

MNXM3

Skipped

MNXM63

Skipped

MNXM51

Skipped

MNXM121

Skipped

MNXM423

Skipped

MNXM6

Skipped

MNXM10

Skipped

MNXM38

Skipped

MNXM208

Skipped

MNXM191

Skipped

MNXM223

Skipped

MNXM7517

Skipped

MNXM12233

Skipped

MNXM558

Skipped

MNXM21

Skipped

MNXM89557

Skipped

Network Topology

Universally Blocked Reactions

122

Orphan Metabolites

Dead-end Metabolites

Stoichiometrically Balanced Cycles

Stoichiometrically Balanced Cycles are artifacts of insufficiently constrained networks resulting in reactions that can carry flux when all the boundaries have been closed. Implementation: Close all model boundary reactions and then use flux variability analysis (FVA) to identify reactions that carry flux.

There are 9 (1.46%) reactions which participate in SBC in the model: SUCD1, GALUi, PGIA, PGI, G6PI, ...

Metabolite Production In Complete Medium

185

Metabolite Consumption In Complete Medium

186

Matrix Conditioning

Ratio Min/Max Non-Zero Coefficients

0.00

Independent Conservation Relations

Rank

506

Degrees Of Freedom

112

Experimental Data Comparison

Growth Prediction

Skipped

Gene Essentiality Prediction

Skipped

Misc. Tests

Environment

Python Version 3.6.12

Platform Linux

Memote Version 0.11.1

Package Versions